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Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence

Subtleties of nanophotonic lithium niobate waveguides for on-chip evanescent wave sensing

Thin-film lithium niobate (TFLN) is promising for optical sensing due to its high nonlinearities, but its material properties present unique design challenges. We compare the sensing performance of the fundamental modes on a TFLN waveguide with a fluorescent dye sample. The TM mode has better overlap with the sample, with a 1.4 × greater sample absorption rate versus the TE mode. However, the TM mode also scatters at a 1.4 × greater rate, yielding less fluorescence overall. The TE mode is, therefore, more appropriate for sensing. Our findings have important implications for TFLN-based sensor designs.

optics

Combined speckle- and propagation-based single shot two-dimensional phase retrieval method

Single-shot two-dimensional (2D) phase retrieval (PR) can recover the phase shift distribution within an object from a single 2D x-ray phase contrast image (XPCI). Two competing XPCI imaging modalities often used for single-shot 2D PR to recover material properties critical for predictive performance capabilities are: speckle-based (SP-XPCI) and propagation-based (PB-XPCI) XPCI imaging. However, PR from SP-XPCI and PB-XPCI images are, respectively, limited to reconstructing accurately slowly and rapidly varying features due to noise and differences in their contrast mechanisms. Herein, we consider a combined speckle- and propagation-based XPCI (SPB-XPCI) image by introducing a mask to generate a reference pattern and imaging in the near-to-holographic regime to induce intensity modulations in the image. We develop a single-shot 2D PR method for SPB-XPCI images of pure phase objects without imposing restrictions such as object support constraints. It is compared against PR methods inspired by those developed for SP-XPCI and PB-XPCI on simulated and experimental images of a thin glass shell before and during shockwave compression. Reconstructed phase maps show improvements in quantitative scores of root-mean-square error and structural similarity index measure using our proposed method.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Improving high temperature resilience of fiber sensor embedded smart components through laser shock peening

This study explores the use of laser shock peening (LSP) to enhance material properties and high-temperature performance of fiber-sensor-fused smart parts fabricated by additive manufacturing (AM) methods. Using embedded fiber sensors as distributed strain gauges, the study demonstrates that LSP can induce compressive strains of up to 130 µε on fiber embedded 1-mm below metal surfaces. The electron backscatter diffraction (EBSD) analysis shows that, with optimized LSP parameters, the metallic matrix undergoes substantial microstructural refinement, resulting in denser structures. Thermal cycling tests showed that the LSP process can increase fiber slippage temperatures by more than 50 °C. This work shows that the LSP process is an effective room-temperature process for enhancing both surface quality and increasing fiber slippage threshold under both thermal and mechanical stress.

Zhong, Shuda [University of Pittsburgh, PA (United

Source Characterization at Low Yields from Physics Experiment One A

The detonation of a well-recorded coupled explosion at the well-characterized Nevada National Security Site, as part of Physics Experiment One, has provided us with an opportunity to compare and contrast methods and results of yield estimation and other event characterization methods. Yield estimates are made using several methods, including local/regional magnitudes, waveform envelopes, acoustic amplitudes, joint seismoacoustic yield, and moment tensors. We include in our analysis a discussion and comparison of applicability, calibrations, assumptions, and uncertainties involved in each. With the exception of magnitude-based methods, all the techniques were more or less successful in recovering the known yield. It is, however, useful to be cognizant of requirements and calibrations, such as station coverage, emplacement conditions, propagation characterization, and uncertainties, to apply the methods to other areas with less complete information. We demonstrate that we can be successful at monitoring low-yield explosions using a variety of methods assuming that the signal-to-noise ratio is adequate at recording stations, and that the material properties are taken into account. Depth estimates are also important, particularly if one allows the possibility of a surface explosion.

Pasyanos, Michael E. [Lawrence Livermore National

Extraction of Vibration Data with Imaging

To date, the primary sensing technology used to measure the vibration response has been accelerometers and strain gages mounted directly to the structure and using either wired or, more recently, wireless telemetry. Cost issues with these sensors and the associated data acquisition systems typically limit the numbers that are deployed on in situ structures. Although there are a few structures with larger sensing counts that in some cases exceed over 1000 sensors, more typical numbers range from ten to one hundred sensors resulting in low spatial resolution when they are applied to physically large systems. When one considers that nuclear power plant structures usually have complex geometries, material properties, connectivity and boundary conditions, it is clear these current approaches to vibration measurements can only provide limited information about a system’s dynamics response characteristics. As an alternative, many non-contact measurement technologies have emerged, including point wise measurement methods such as Global Positioning System (GPS), microwave interferometry, and laser Doppler vibrometry (LDV), as well as simultaneous full-field measurement methods such as electronic speckle pattern interferometry, holography interferometry, and muon tomography, some of which can provide high spatial resolution measurements. Among these methods, digital video imaging techniques have emerged as a feasible solution for full-field vibration measurements that provide significantly more detailed dynamic response information because every pixel becomes a measurement point. Furthermore, recent advances in image processing and computer vision algorithms have been successfully used to process video data for experimental and operational modal analysis. Such full-field measurements have the potential to significantly improve many current structural assessment procedures including system identification (modal parameter estimation), structural health monitoring, load reconstruction, model validation, and model updating. Furthermore, more recent full-field imaging techniques can be accomplished with relatively low-cost, commercially-available off-the-shelf cameras. However, these measurement procedures have other limitations that must be considered such as the ability to only measure visibly accessible points on a structure and a more limited dynamic range and bandwidth than can be achieved with accelerometers or strain gages.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND

Milestone report for MRT 8504: Commission EXAFS spectrometer with spectral range of 17.95-18.6 keV design to obtain EXAFS data for Pu L shell experiments

This milestone describes the development and fielding of EXAFS Phase II spectrometer designed to provide high quality (SNR>=5) EXAFS spectra for Plutonium measurements at the National Ignition facility (NIF). Benefits: the EXAFS data will be used by the High Energy Density (HED) Physics and more specifically the Focused Material Science program to measure the thermal state of compressed materials with good temperature sensitivity (~100-1000 Kelvin). Data with good signal to noise ratio (SNR>=5) and good spectral resolution allows the FMS program to fill a gap in diagnosing temperature to completely constrain material properties for weapon physics and Stockpile Stewardship applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND

Cavity Based Searches for New Particles and Gravitational Waves

The Superconducting Quantum Materials and Systems Center, led by Fermi National Accelerator Laboratory, is one of five research centers funded by the U.S. Department of Energy as part of a national initiative to develop and deploy the world’s most powerful quantum computers and sensors. The SQMS Center uses world-record quality-factor superconducting radio-frequency, or SRF, cavities as ultra-sensitive quantum probes. Within the quantum sensing thrust, researchers are developing experiments based on cavities and novel quantum devices to search for particles beyond the Standard Model, dark matter candidates, gravitational waves and fundamental material properties. The seminar will focus mostly on Dark SRF and MAGO activities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

LYNM PE1 Pre-Experiment A Site Characterization Report

Underground chemical explosive experiments such as LYNM PE1 generate large multiphenomenological datasets, require complex site preparation and build out, and utilize cutting edge models and analysis techniques to analyze and simulate the explosion-induced signals. This wide range of outcomes makes it a necessity to thoroughly characterize the testbed in advance of experiments in a way that complements the wide suite of data being generated. Here, we present a broad overview of the site characterization work and data collection that was conducted before Experiment A, which is the first in a series of three PE1 experiments. This work includes, but is not limited to, geologic mapping, physical sample collection, analysis of material properties, geophysical borehole logging, and in-situ measurements. This information was collected by a large, dedicated team and was used to inform site construction, finalize instrumentation placement, generate Geologic Framework Models, feed pre-experiment predictions, and facilitate post-experiment data analysis

58 GEOSCIENCES

Material exploration towards high quality factor microwave resonators

Niobium and aluminum have been widely used to realize superconducting resonators and qubits. However, the native oxide at the metal air interface limits the devices results. This layer is highly disordered, and it induces losses limiting the performances of the resonators or qubits. Recently, tantalum led to great improvement in qubit relaxation time. This improvement has been attributed to a thinner and less disordered oxide layer compared to Nb and Al. This study is aimed to limit the formation of the oxide layer, by the introduction of novel superconducting materials such as rhenium or by encapsulating the Nb surface with other superconducting materials such as Ta, Al, Re or other non-superconducting materials such as Au. To better understand the results, we are realizing these studies on coplanar waveguide resonators where the relation between surface losses and quality factor is clear. We are also analyzing different fabrication techniques to completely characterize our devices, linking material properties to the performances. In this work we are also varying the participation ratio of the devices in order to extract with higher fidelity and precision the losses introduced by the involved interfaces.

Crisa, F.

MOOSE-Workbench integration and MOOSE meshing capability enhancements to facilitate inputs and outputs for multiphysics modeling

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is an open-source framework that supports many of the US Department of Energy’s (DOE’s) Nuclear Energy Advanced Modeling and Simulation (NEAMS) technical areas (TA). These TAs develop and use NEAMS physics and coupling modules in multiple ways to enable the research and development of complex physics models. In addition to the MOOSE framework, the NEAMS Workbench user interface provides a common analysis environment with user-interaction accelerators that streamline the tasks of model creation, review, execution, and out put inspection. In FY 2024, objectives were realized in the MOOSE framework application development support and user-oriented improvements. Application development improvements support both developers and users with an expanded Reactor Module and Mesh System, stateful material property support for mortar contact, and customizable convergence criteria. Additionally, new user-oriented features were implemented in the MOOSE framework language server, including autocompletion snippets, definition from source and find reference navigations, and syntax overrides. Lastly, improvements were made to the input interpreter necessary to support the MOOSE language server and the NEAMS Workbench so that they can interact with syntactically incomplete user inputs. These improvements and more were intended to address stakeholder feedback and improve developer and user ability to conduct advanced nuclear energy modeling and simulation in support of DOE and industry needs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Development of integrated neutronics and thermal analysis capabilities to support design and optimization of fusion engineering demonstration facility systems and blanket design (Final Scientific/Technical Report)

A fusion engineering demonstration facility would be the first step in the commercial fusion plant developmental pathway that aims to be an engineering demonstration of tritium self-sufficiency. One of the primary requirements for tritium self-sufficiency, as well as to ensure low plant tritium release to the external environment, is to minimize the tritium loss through the internal components, which requires accurate predictions of the tritium behavior for a wide range of materials and system conditions. This grant addressed the lack of a comprehensive model which accounts for particular conditions, such as the significance of temperature fields and neutronics information, and the systematic uncertainty quantification of associated material properties that impact tritium generation, utilization, and loss mechanisms in the blanket.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Development of integrated neutronics and thermal analysis capabilities to support design and optimization of fusion engineering demonstration facility systems and blanket design (Final Scientific/Technical Report)

A fusion engineering demonstration facility would be the first step in the commercial fusion plant developmental pathway that aims to be an engineering demonstration of tritium self- sufficiency. One of the primary requirements for tritium self-sufficiency, as well as to ensure low plant tritium release to the external environment, is to minimize the tritium loss through the internal components, which requires accurate predictions of the tritium behavior for a wide range of materials and system conditions. This grant addressed the lack of a comprehensive model which accounts for particular conditions, such as the significance of temperature fields and neutronics information, and the systematic uncertainty quantification of associated material properties that impact tritium generation, utilization, and loss mechanisms in the blanket.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

DECOVALEX-2023: Task C Final Report

The Full-scale Emplacement (FE) heater experiment at the Mont Terri Underground Rock Laboratory (URL) was designed and conducted by Nagra to replicate an emplacement tunnel of Nagra’s reference repository design at 1:1 scale. Alongside testing the technical feasibility of constructing disposal tunnels, emplacing waste containers in the tunnels and then backfilling them, the main goals of the FE experiment are (1) to obtain a better understanding of the coupled effects of induced thermo-hydro-mechanical (THM) processes that may occur and (2) to validate existing coupled THM models (Müller et al., 2017). A key aspect of ensuring safety for repositories located in low-permeability rock involves minimizing any damage to the rock itself, thereby preserving its integrity and promoting a stable environment Amongst a number of processes that could damage the rock is the increase in pore pressure due to thermal loading caused by heat emitted from the waste. To reduce the potential damage of the rock, it is important to analyse the evolution of heat over time due to the heat load of the containers and assess possible consequences by coupled THM models. The aim of Task C of DECOVALEX-2023 was to build 3D numerical models of the FE experiment, focussing in particular on the heating induced pore pressure change in the Opalinus Clay. Data from a large number of sensors were available from the FE experiment for model comparison. These sensors measured temperature and relative humidity in the bentonite around the heaters, and temperature, pressure and displacement/strain in the surrounding Opalinus clay. Data were available from the start of excavation (April 2012) up to August 2020 for most sensors (more than 5 years from the start of heating in December 2014). To fulfil the overall aim of the task, the work was broken down into a number of steps, starting with simpler models to build confidence in each team’s approach and then moving to more complex models that better represent the FE experiment. Step 0 consisted of 2D benchmark models, gradually increasing the number of processes that are represented from thermal (T) only models in Step 0a, to coupled thermal hydraulic (TH) models in Step 0b with a representation of changing porosity, to coupled thermo-hydro-mechanical (THM) models in Step 0c, where porosity changes are calculated by the mechanical model. A detailed specification of processes, parameters, initial and boundary conditions was provided for this step, with the ambition that all teams would work towards close agreement in their model results, thus building confidence in the model implementations. vi It was not straightforward to achieve agreement between the teams, so additional steps (Step 0b2, 0b3, 0c2, 0c3) were added along with derivation of some analytical solutions against which the models could be compared. The reasons for the differences between teams were investigated and found to be caused primarily by different conceptual model assumptions (including temperature dependence of the thermal expansion of water), different model formulations (including porosity evolution) and differences in modelled domain sizes, boundary conditions and grid discretisation. This demonstrates that comparisons between multiple modelling teams and/or comparison with analytical results and experimental data are highly beneficial in providing an indication of uncertainty in model predictions. At the conclusion of Step 0, almost all teams had achieved a close agreement in model results and those that had not achieved an agreement knew the reason for this. Step 1 moved from 2D models to 3D models of the FE experiment without adding technical features like shotcrete or EDZ, and only considering the heating phase. Initially the 3D model was tightly specified to continue to build confidence in the model implementations (Step 1a). The results of Step 1a were compared to the data from the FE-experiment without the teams seeing the data. The teams were then provided with a sub-set of the data from the FE-experiment and invited to consider how best to use the large dataset for model comparison (Step 1b). Teams were then asked to use the data provided to calibrate their models, only changing material property values rather than adding features or processes to their models (Step 1c). In Step 1, teams were asked to only model the heating phase of the experiment, so pressure in the Opalinus Clay was reported as change in pressure since the initial conditions were specified rather than modelled. The change from 2D to 3D models was accompanied by an increase in the dispersion of results between the teams. Some of this was resolved during the task, but some remained and is potentially due to model discretisation. Calibration of parameters was useful in improving the fit of the models to the data but the remaining differences indicated that the models were missing features or processes. In Step 2, the teams were asked to update their models with additional features and processes as well as calibrating parameters to try and improve the fit of the models to the data. Teams were encouraged to represent ventilation of the open FE tunnel prior to backfilling with heaters and bentonite and in Step 2, the absolute pressure in the Opalinus Clay was compared between the teams. Teams took different approaches, but there was consideration of adding shotcrete and an EDZ into the model, representing stress change during excavation and different approaches to modelling ventilation of the FE tunnel. Overall, the documented results showed a very good agreement for temperature. The results for porewater pressure evolution showed a significant improvement for most teams compared to Step 1c with a good agreement to the measurements for several teams whereas some teams overpredicted the pressure increase and others overpredicted the drainage effect especially for the sensors close to the heater. Step 3 was an opportunity for teams to use the models developed in Step 1 and Step 2 to make predictions about the temperature and pressure changes that will be expected at the FE experiment over the next few years in light of the planned changes in thermal output of the heaters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W

DASSH-F: Subchannel Based Thermal Analysis

The DASSH thermal analysis code is designed to rapidly allow a reactor design engineer to obtain flow rates requirements that satisfy peak temperature constraints in the domain. The advantage of using DASSH over a hand calculation is that it has a more rigorous treatment of the pin power distribution and coolant heat transfer within an assembly and between assemblies. The advantage of using DASSH over a conventional 3D subchannel code or a computational fluid dynamics code (CFD) is that it can obtain the desired solution in a matter of minutes in serial with minor computer memory needs. The DASSH methodology is virtually identical to SUPERENERGY-2 with additional functionalities taken from follow on work to SUPERENERGY-2 done at ANL in the 1980s. DASSH today is an integral component of the Argonne Fast Reactor analysis suite for reactor design work. DASSH obtains the power distribution from a coupled neutron-gamma heating calculation in GAMSOR (including DIF3D) at each time point of a companion fuel cycle analysis calculation with REBUS. The domain in DASSH assumes a hexagonal grid typical for fast reactors with much of the geometry information taken from the DIF3D model. DASSH assumes the assemblies that are loaded into each grid position are ducted to control the coolant flow. Considerable detail is given on the subchannel formulation of DASSH in this document. Much of the formulation and design of the code builds upon research done by previous authors with little new investigation. Thus the decisions made in developing the subchannel model used in DASSH have their origins over 50 years ago. Much of the heat transfer methodology in DASSH is built upon correlations for both the coolant mixing and heat transfer coefficients for pins and ducts. DASSH is thus not a rigorous treatment of a given problem, but a rapid assessment of the temperature field that has known limitations with respect to an experimental measurement or CFD calculation. The DASSH input and output are detailed along with usage of the software. The DASSH output provides tables of evaluated material properties and key coolant and pin temperature results. DASSH can create Python scripts that generate domain summary pictures. DASSH can also generate assembly temperature maps and VTK output files which allow the DASSH solution to be visualized. As the primary purpose of the DASSH software is to compute the coolant and fuel pin temperature distribution for a given model of a reactor, much of the output focus is giving the user quick summary tables needed to assess the performance of a given orifice flow specification. The present version of DASSH has a crude orifice search capability and an efficient orifice flow search capability. The flow search tries to meet user specified constraints for 1) peak 2-sigma clad midwall temperature, 2) peak coolant temperature, and 3) desired bulk outlet temperature. There are many development shortcomings in DASSH detailed in this document, but this version is functional for modern analysis needs. This document serves as the manual for the Fortran based DASSH software that was developed to replace the Python version of DASSH developed as part of the VTR program.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Electrochemical Production of Highly Valuable Carbon Nanotubes from Flue-Gas Sourced CO 2

The overarching goal of the project was to demonstrate a technology at pilot-scale that enables a net reduction in CO 2 and the production of carbon nanotubes (CNTs) with material properties comparable to commercially available CNTs at a selling price of ~80-90% less than what is available in the current market. The objectives were: (1) demonstrate the ability to utilize synthetic and real flue gas provided by a utility to produce CNTs through the SkyNano’s novel electrochemical process; (2) produce CNTs at the pilot-scale (0.2 kg/hr) using industrial flue gas that exhibit properties consistent with those available on the market today in industrial quantities, including median diameters of <30 nm, purity of at least 95% CNTs in final product, and high crystallinity (I D /I G < 1, measured via Raman spectroscopy); and (3) demonstrate the process to be sustainable and economically viable through the completion of a techno-economic analysis (TEA) and a life-cycle analysis (LCA).

20 FOSSIL-FUELED POWER PLANTS

Machine Learning for Automated Weld Quality Monitoring and Control

Resistance Spot Welding (RSW) is a critical process in the automotive industry, valued for its cost-effectiveness, short cycle time, and robustness. However, achieving consistent high-quality joints remains challenging due to the complex interplay of various factors, like materials, processes, and manufacturing uncertainties, etc. Under the collaborative project between Oak Ridge National Laboratory (ORNL) and General Motors (GM), we have developed a robust and expansible machine learning (ML) framework aimed at enhancing quality control in RSW. By harnessing the power of machine learning, we have developed the ability to ensure every aspect of the welding process, from the initial process design stage to the final weld joint quality. The framework operates by analyzing a variety of data streams, including in-line process signals, process parameters, materials, and postprocessed weld joint data. Through this analysis, the models have been trained to detect deviations from optimal quality standards, leveraging their ability to identify signature data patterns and anomalies within in-line signals and construct complex correlations between these signals and weld quality parameters. Meanwhile, the machine learning framework is designed to adapt to a variety of materials, including high strength steels and aluminum alloys, etc. Its flexible architecture facilitates the incorporation of diverse data sources and features, enabling precise modeling and prediction across a broad range of material properties and weld quality variables. The expansible ML frameworks represent a promising transformation in weld quality monitoring and control, empowering industry to achieve high levels of efficiency, consistency, and reliability in manufacturing.

99 GENERAL AND MISCELLANEOUS

Investigation of the Mechanical Degradation of Zinc-Based Cold Spray Coatings for Steel Pipelines

Internal corrosion in wet natural gas is a big challenge in the oil and gas industry due to corrosive constituents such as carbon dioxide (CO2), hydrogen sulfide (H2S), other forms of sulfur, and water in the gas stream. To mitigate internal corrosion, zinc-based cold spray coatings were designed for use in natural gas pipelines to increase the lifespan of the pipeline network. However, one of the requirements in designing internal coatings is the resistance of the coatings to mechanical forces applied on the pipeline's internal wall during pigging operations. These forces are primarily compressive and shear/friction forces. This study examines material properties that must be considered when evaluating mechanical considerations.

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